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Detailed information for vg1009328992:

Variant ID: vg1009328992 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 9328992
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:


AGTCTGCAGAGATCAGCTGATCGGTCAGTTCATCATCAAAACTAGACATGAACTTCTCCTACCTCTCAGCATTGGTGTGCAGGTCGTTAGGGACGTAGTG[C/T]
GCAAGGCGGTTGAACTCATGCAGATACTATGTATCTGTCATGTCTCCTTGATGCAGTGCACGAAACTTCCTCTTCTTTTGTGCACGGGACTTCCTCTTCT

Reverse complement sequence

AGAAGAGGAAGTCCCGTGCACAAAAGAAGAGGAAGTTTCGTGCACTGCATCAAGGAGACATGACAGATACATAGTATCTGCATGAGTTCAACCGCCTTGC[G/A]
CACTACGTCCCTAACGACCTGCACACCAATGCTGAGAGGTAGGAGAAGTTCATGTCTAGTTTTGATGATGAACTGACCGATCAGCTGATCTCTGCAGACT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 3.20% 0.00% 0.00% NA
All Indica  2759 98.10% 1.90% 0.00% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 65.10% 34.90% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.20% 1.80% 0.00% 0.00% NA
Indica Intermediate  786 96.70% 3.30% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 1.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1009328992 C -> T LOC_Os10g18360.1 upstream_gene_variant ; 1056.0bp to feature; MODIFIER silent_mutation Average:63.64; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg1009328992 C -> T LOC_Os10g18364.1 upstream_gene_variant ; 1653.0bp to feature; MODIFIER silent_mutation Average:63.64; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N
vg1009328992 C -> T LOC_Os10g18360-LOC_Os10g18364 intergenic_region ; MODIFIER silent_mutation Average:63.64; most accessible tissue: Zhenshan97 young leaf, score: 88.995 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1009328992 2.46E-08 NA mr1261 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1009328992 NA 7.15E-06 mr1654 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251